Processing a taxatable post MBC and illumina_post_MBC_script2.R

things this script should do

#load taxatable(s)
#load single mastersheet
#subset the mastersheet if desired
##if using subset mastersheet, use only subset taxatable (or merged taxatable if >1 supplied)
#show summary: taxa list, sum of reads, min and max reads in a sample, no. samples

settings

#if multiple, will be merged
taxatabs<-c("/mnt/Disk1/BASTIAN_POST_MBC_MISEQS/FILTURB_12S_BLAST/FILTURB-2018_07_12S.none.flash2.vsearch_qfilt.cutadapt.vsearch_uniq.vsearch_afilt.allsamples_step5.ALL_vsearch_uniq.nodenoise.noclust.taxatable.tf.spliced.txt")

#filturb datasheet
ss_url<-"https://docs.google.com/spreadsheets/d/1FUSaeVaYzms2EOGUoCAB4jaRKzguD3AKTsC8lYwaKP4/edit?ts=5dae01be#gid=1531090624"

#options for subsetting master sheet 
subsetlist<-list(experiment_id=c("2018_07"), Primer_set=c("12SV5.2"),study=c("South"))

bastoolsDir<-"/home/bastian.egeter/git_bastools/bastools/"

#sample_type for "real" samples (not negatives)
real=c("Field")

#columns in master sheet to make barplots of
columns=c("biomaterial","sample_type","Site")

#print taxon tables for negatives (even if not printed, plots will still be made)
printnegs=F

#print taxon tables for removal of contaminants
printcontaminations=F

#group code to remove contaminants based on negatives. e.g. for water field negatives, group code is probably site or something similar. For extraction negatives it is probably extraction batch etc. This should be improved to handle multiple codes
group.code="Site"

load functions

setwd(bastoolsDir)
source("master_functions.R")
library(ggplot2)
library(googlesheets4)
sheets_auth(email = "basegeter@gmail.com")
options(httr_oob_default = TRUE)

organise mastersheet

## Reading from 'FILTURB_datasheet'

## Range "'Master_Samplesheet'"

## Showing xtabs for entire datasheet, including Sample_Type by default

## , , Primer_set = 12SV5.2, study = Both
## 
##                      experiment_id
## sample_type           2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
##   Extraction_Negative       0       0       0          0      0
##   Field                     0       0       0          0      0
##   Field_Negative            0       0       0          0      0
##   PCR_negative              0       0       0          0      0
##   Tissue                    0       0       2          0      0
## 
## , , Primer_set = 12SV51, study = Both
## 
##                      experiment_id
## sample_type           2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
##   Extraction_Negative       0       0       0          0      0
##   Field                     0       0       0          0      0
##   Field_Negative            0       0       0          0      0
##   PCR_negative              0       0       0          0      0
##   Tissue                    0       0       2          0      4
## 
## , , Primer_set = LERAY-XT, study = Both
## 
##                      experiment_id
## sample_type           2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
##   Extraction_Negative       0       0       0          0      0
##   Field                     0       0       0          0      0
##   Field_Negative            0       0       0          0      0
##   PCR_negative              0       0       0          0      0
##   Tissue                    0       0       0          0      0
## 
## , , Primer_set = 12SV5.2, study = North
## 
##                      experiment_id
## sample_type           2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
##   Extraction_Negative       0       2       0          0      0
##   Field                     0      23       0          0      0
##   Field_Negative            0       0       0          0      0
##   PCR_negative              0       0       1          0      0
##   Tissue                    0       0       0          0      0
## 
## , , Primer_set = 12SV51, study = North
## 
##                      experiment_id
## sample_type           2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
##   Extraction_Negative       0       0      12          0      0
##   Field                     0       1     114          0      0
##   Field_Negative            0       0      40          0      0
##   PCR_negative              4       1       3          0      0
##   Tissue                    0       0       0          0      0
## 
## , , Primer_set = LERAY-XT, study = North
## 
##                      experiment_id
## sample_type           2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
##   Extraction_Negative       0       0       0          0      0
##   Field                     0       0       0         72      0
##   Field_Negative            0       0       0          0      0
##   PCR_negative              0       0       0          0      0
##   Tissue                    0       0       0          0      0
## 
## , , Primer_set = 12SV5.2, study = South
## 
##                      experiment_id
## sample_type           2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
##   Extraction_Negative       0       0      10          0      0
##   Field                     0       0     194          0      0
##   Field_Negative            0       0      32          0      0
##   PCR_negative              0       0       5          0      0
##   Tissue                    0       0       0          0      0
## 
## , , Primer_set = 12SV51, study = South
## 
##                      experiment_id
## sample_type           2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
##   Extraction_Negative       0       0      10          0      0
##   Field                     0       0     194          0      0
##   Field_Negative            0       0      32          0      0
##   PCR_negative              0       0       4          0      0
##   Tissue                    0       0       0          0      0
## 
## , , Primer_set = LERAY-XT, study = South
## 
##                      experiment_id
## sample_type           2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
##   Extraction_Negative       0       0       0          0      0
##   Field                     0       0       0         64      0
##   Field_Negative            0       0       0          6      0
##   PCR_negative              0       0       0          2      0
##   Tissue                    0       0       0          0      0
## 
## , , Primer_set = 12SV5.2, study = Test
## 
##                      experiment_id
## sample_type           2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
##   Extraction_Negative       0       0       0          0      0
##   Field                     0       0       0          0      0
##   Field_Negative            0       0       0          0      0
##   PCR_negative              0       0       0          0      0
##   Tissue                    0       0       0          0      0
## 
## , , Primer_set = 12SV51, study = Test
## 
##                      experiment_id
## sample_type           2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
##   Extraction_Negative       0       0       0          0      0
##   Field                    14       0       0          0      0
##   Field_Negative            0       0       0          0      0
##   PCR_negative              2       0       0          0      0
##   Tissue                    0       0       0          0      0
## 
## , , Primer_set = LERAY-XT, study = Test
## 
##                      experiment_id
## sample_type           2018_02 2018_04 2018_07 HSJUN19BAS SANG_1
##   Extraction_Negative       0       0       0          0      0
##   Field                     0       0       0          0      0
##   Field_Negative            0       0       0          0      0
##   PCR_negative              0       0       0          0      0
##   Tissue                    0       0       0          0      0

## Subsetting datasheet, check output to see if it made sense

## $experiment_id
## [1] "2018_07"
## 
## $Primer_set
## [1] "12SV5.2"
## 
## $study
## [1] "South"

## , , Primer_set = 12SV5.2, study = South
## 
##                      experiment_id
## sample_type           2018_07
##   Extraction_Negative      10
##   Field                   194
##   Field_Negative           32
##   PCR_negative              5

import taxtabs and subset

## Loading required package: tidyverse

## ── Attaching packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──

## ✔ tibble  2.1.3     ✔ purrr   0.3.2
## ✔ tidyr   0.8.3     ✔ dplyr   0.8.3
## ✔ readr   1.3.1     ✔ stringr 1.4.0
## ✔ tibble  2.1.3     ✔ forcats 0.4.0

## ── Conflicts ────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()

## /mnt/Disk1/BASTIAN_POST_MBC_MISEQS/FILTURB_12S_BLAST/FILTURB-2018_07_12S.none.flash2.vsearch_qfilt.cutadapt.vsearch_uniq.vsearch_afilt.allsamples_step5.ALL_vsearch_uniq.nodenoise.noclust.taxatable.tf.spliced.txt

## reads: 5349423, taxa: 35, samples: 638

## Read counts all good

## merged taxatable

## reads: 5349423, taxa: 35, samples: 638

make new taxa table based on subsetted master sheet

## Removing taxa/samples with 0 reads

## Showing summary of detections

## Loading required package: plotly

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
## 
##     layout

remove the NAs and no_hits

## 2 'NA' reads removed

## 1068818 'No_hits' reads removed

reads & dxns by rank

##           rank  reads percent
## 1 above_family   9860     1.0
## 2       family  18362     1.9
## 3        genus  16455     1.7
## 4      species 910459    95.3

##           rank dxns percent
## 1 above_family    8     1.5
## 2       family  139    25.9
## 3        genus  179    33.3
## 4      species  211    39.3

detection distribution

## Using taxon as id variables

## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

krona plot

Download FILTURB-2018_07_12S.none.flash2.vsearch_qfilt.cutadapt.vsearch_uniq.vsearch_afilt.allsamples_step5.ALL_vsearch_uniq.nodenoise.noclust.taxatable.tf.spliced.krona.html

stack plots (select top 30 taxa?)

## Plotting taxatable according to selected master sheet columns, values=reads, plotted as %

## Using taxon as id variables

## Outputting as a list where first element is plot and second is legend

## Using taxon as id variables

## Outputting as a list where first element is plot and second is legend

## Using taxon as id variables
## Outputting as a list where first element is plot and second is legend

## Plotting taxatable according to selected master sheet columns, values=reads, plotted as raw

## Using taxon as id variables

## Outputting as a list where first element is plot and second is legend

## Using taxon as id variables

## Outputting as a list where first element is plot and second is legend

## Using taxon as id variables
## Outputting as a list where first element is plot and second is legend

## Plotting taxatable according to selected master sheet columns, values=detections,plotted as raw

## Using taxon as id variables

## Outputting as a list where first element is plot and second is legend

## Using taxon as id variables

## Outputting as a list where first element is plot and second is legend

## Using taxon as id variables
## Outputting as a list where first element is plot and second is legend

check negatives

## Hiding tabular output of negatives

## Ignoring the following taxa: NA;NA;NA;NA;NA;NA;NA & no_hits;no_hits;no_hits;no_hits;no_hits;no_hits;no_hits

## from 32 Field_Negative samples 12 contained reads

## from 5 PCR_negative samples 0 contained reads

## from 10 Extraction_Negative samples 1 contained reads

## Plotting Field_Negative

## Using taxon as id variables

## No master_sheet or column specified, making default plot

## Plotting PCR_negative

## Plotting Extraction_Negative

## Using taxon as id variables

## No master_sheet or column specified, making default plot

test removing contaminants blindly

## Based on Field_Negative FILTURB-F100-A-N4-12S2-2018_07 , Removing detections of

## [1] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;Alytes obstetricans"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;NA"                 
## [3] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;NA;NA"

## from

##  [1] "FILTURB-F95-A-N3-12S2-2018_07"  "FILTURB-F96-A-N3-12S2-2018_07" 
##  [3] "FILTURB-F97-A-N3-12S2-2018_07"  "FILTURB-F98-A-N3-12S2-2018_07" 
##  [5] "FILTURB-F99-A-N3-12S2-2018_07"  "FILTURB-F100-A-N3-12S2-2018_07"
##  [7] "FILTURB-C33-A-N3-12S2-2018_07"  "FILTURB-F95-A-N4-12S2-2018_07" 
##  [9] "FILTURB-F96-A-N4-12S2-2018_07"  "FILTURB-F97-A-N4-12S2-2018_07" 
## [11] "FILTURB-F98-A-N4-12S2-2018_07"  "FILTURB-F99-A-N4-12S2-2018_07" 
## [13] "FILTURB-F100-A-N4-12S2-2018_07" "FILTURB-C33-A-N4-12S2-2018_07"

## which all belong to Site : B06a

## 12665 reads removed from 3 detection(s) in 1 sample(s), of which 12665 were in the negative. See table below for details:

## Not printing contamination table

## Based on Field_Negative FILTURB-F106-A-N4-12S2-2018_07 , Removing detections of

## [1] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;Alytes obstetricans"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;NA"

## from

##  [1] "FILTURB-F101-A-N3-12S2-2018_07" "FILTURB-F103-A-N3-12S2-2018_07"
##  [3] "FILTURB-F104-A-N3-12S2-2018_07" "FILTURB-F106-A-N3-12S2-2018_07"
##  [5] "FILTURB-C34-A-N3-12S2-2018_07"  "FILTURB-F102-A-N3-12S2-2018_07"
##  [7] "FILTURB-F105-A-N3-12S2-2018_07" "FILTURB-F101-A-N4-12S2-2018_07"
##  [9] "FILTURB-F103-A-N4-12S2-2018_07" "FILTURB-F104-A-N4-12S2-2018_07"
## [11] "FILTURB-F106-A-N4-12S2-2018_07" "FILTURB-C34-A-N4-12S2-2018_07" 
## [13] "FILTURB-F102-A-N4-12S2-2018_07" "FILTURB-F105-A-N4-12S2-2018_07"

## which all belong to Site : B20a

## 3905 reads removed from 2 detection(s) in 1 sample(s), of which 3905 were in the negative. See table below for details:

## Not printing contamination table

## Based on Field_Negative FILTURB-F125-A-N3-12S2-2018_07 , Removing detections of

## [1] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;Alytes obstetricans"          
## [2] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;NA"                           
## [3] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Lissotriton;NA"               
## [4] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;NA;NA"                        
## [5] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Pleurodeles;NA"               
## [6] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Pleurodeles;Pleurodeles waltl"

## from

##  [1] "FILTURB-F119-A-N3-12S2-2018_07" "FILTURB-F120-A-N3-12S2-2018_07"
##  [3] "FILTURB-F121-A-N3-12S2-2018_07" "FILTURB-F122-A-N3-12S2-2018_07"
##  [5] "FILTURB-F123-A-N3-12S2-2018_07" "FILTURB-C37-A-N3-12S2-2018_07" 
##  [7] "FILTURB-F125-A-N3-12S2-2018_07" "FILTURB-F124-A-N3-12S2-2018_07"
##  [9] "FILTURB-F119-A-N4-12S2-2018_07" "FILTURB-F120-A-N4-12S2-2018_07"
## [11] "FILTURB-F121-A-N4-12S2-2018_07" "FILTURB-F122-A-N4-12S2-2018_07"
## [13] "FILTURB-F123-A-N4-12S2-2018_07" "FILTURB-C37-A-N4-12S2-2018_07" 
## [15] "FILTURB-F125-A-N4-12S2-2018_07" "FILTURB-F124-A-N4-12S2-2018_07"

## which all belong to Site : A01

## 9393 reads removed from 24 detection(s) in 7 sample(s), of which 3196 were in the negative. See table below for details:

## Not printing contamination table

## Based on Field_Negative FILTURB-F125-A-N4-12S2-2018_07 , Removing detections of

##  [1] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;Alytes obstetricans"             
##  [2] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;NA"                              
##  [3] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Discoglossus;NA"                        
##  [4] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;NA;NA"                                  
##  [5] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;Hyla meridionalis"                  
##  [6] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;NA"                                 
##  [7] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;NA;NA"                           
##  [8] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Salamandra;NA"                   
##  [9] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Salamandra;Salamandra salamandra"
## [10] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Triturus;NA"                     
## [11] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Triturus;Triturus marmoratus"    
## [12] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Triturus;Triturus pygmaeus"      
## [13] "Eukaryota;Chordata;Amphibia;unknown;NA;NA;NA"

## from

##  [1] "FILTURB-F119-A-N3-12S2-2018_07" "FILTURB-F120-A-N3-12S2-2018_07"
##  [3] "FILTURB-F121-A-N3-12S2-2018_07" "FILTURB-F122-A-N3-12S2-2018_07"
##  [5] "FILTURB-F123-A-N3-12S2-2018_07" "FILTURB-C37-A-N3-12S2-2018_07" 
##  [7] "FILTURB-F125-A-N3-12S2-2018_07" "FILTURB-F124-A-N3-12S2-2018_07"
##  [9] "FILTURB-F119-A-N4-12S2-2018_07" "FILTURB-F120-A-N4-12S2-2018_07"
## [11] "FILTURB-F121-A-N4-12S2-2018_07" "FILTURB-F122-A-N4-12S2-2018_07"
## [13] "FILTURB-F123-A-N4-12S2-2018_07" "FILTURB-C37-A-N4-12S2-2018_07" 
## [15] "FILTURB-F125-A-N4-12S2-2018_07" "FILTURB-F124-A-N4-12S2-2018_07"

## which all belong to Site : A01

## 24066 reads removed from 27 detection(s) in 8 sample(s), of which 8826 were in the negative. See table below for details:

## Not printing contamination table

## Based on Field_Negative FILTURB-F34-A-N3-12S2-2018_07 , Removing detections of

## [1] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;NA;NA"
## [2] "Eukaryota;Chordata;Amphibia;Anura;NA;NA;NA"

## from

##  [1] "FILTURB-F29-A-N3-12S2-2018_07" "FILTURB-F30-A-N3-12S2-2018_07"
##  [3] "FILTURB-F31-A-N3-12S2-2018_07" "FILTURB-F32-A-N3-12S2-2018_07"
##  [5] "FILTURB-F33-A-N3-12S2-2018_07" "FILTURB-F34-A-N3-12S2-2018_07"
##  [7] "FILTURB-C22-A-N3-12S2-2018_07" "FILTURB-F29-A-N4-12S2-2018_07"
##  [9] "FILTURB-F30-A-N4-12S2-2018_07" "FILTURB-F31-A-N4-12S2-2018_07"
## [11] "FILTURB-F32-A-N4-12S2-2018_07" "FILTURB-F33-A-N4-12S2-2018_07"
## [13] "FILTURB-F34-A-N4-12S2-2018_07" "FILTURB-C22-A-N4-12S2-2018_07"

## which all belong to Site : G21

## 3990 reads removed from 7 detection(s) in 6 sample(s), of which 3756 were in the negative. See table below for details:

## Not printing contamination table

## Based on Field_Negative FILTURB-F40-A-N4-12S2-2018_07 , Removing detections of

## [1] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;Hyla meridionalis"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;NA"

## from

##  [1] "FILTURB-F35-A-N3-12S2-2018_07" "FILTURB-F36-A-N3-12S2-2018_07"
##  [3] "FILTURB-F37-A-N3-12S2-2018_07" "FILTURB-F38-A-N3-12S2-2018_07"
##  [5] "FILTURB-F39-A-N3-12S2-2018_07" "FILTURB-F40-A-N3-12S2-2018_07"
##  [7] "FILTURB-C23-A-N3-12S2-2018_07" "FILTURB-F35-A-N4-12S2-2018_07"
##  [9] "FILTURB-F36-A-N4-12S2-2018_07" "FILTURB-F37-A-N4-12S2-2018_07"
## [11] "FILTURB-F38-A-N4-12S2-2018_07" "FILTURB-F39-A-N4-12S2-2018_07"
## [13] "FILTURB-F40-A-N4-12S2-2018_07" "FILTURB-C23-A-N4-12S2-2018_07"

## which all belong to Site : G35

## 70665 reads removed from 21 detection(s) in 12 sample(s), of which 4445 were in the negative. See table below for details:

## Not printing contamination table

## Based on Field_Negative FILTURB-F46-A-N4-12S2-2018_07 , Removing detections of

## [1] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;Alytes obstetricans"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;Alytes;NA"                 
## [3] "Eukaryota;Chordata;Amphibia;Anura;Alytidae;NA;NA"                     
## [4] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;Hyla meridionalis"     
## [5] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;NA"                    
## [6] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;NA;NA"

## from

##  [1] "FILTURB-F41-A-N3-12S2-2018_07" "FILTURB-F42-A-N3-12S2-2018_07"
##  [3] "FILTURB-F43-A-N3-12S2-2018_07" "FILTURB-F44-A-N3-12S2-2018_07"
##  [5] "FILTURB-F45-A-N3-12S2-2018_07" "FILTURB-F46-A-N3-12S2-2018_07"
##  [7] "FILTURB-C24-A-N3-12S2-2018_07" "FILTURB-F41-A-N4-12S2-2018_07"
##  [9] "FILTURB-F42-A-N4-12S2-2018_07" "FILTURB-F43-A-N4-12S2-2018_07"
## [11] "FILTURB-F44-A-N4-12S2-2018_07" "FILTURB-F45-A-N4-12S2-2018_07"
## [13] "FILTURB-F46-A-N4-12S2-2018_07" "FILTURB-C24-A-N4-12S2-2018_07"

## which all belong to Site : G16

## 76062 reads removed from 29 detection(s) in 9 sample(s), of which 12151 were in the negative. See table below for details:

## Not printing contamination table

## Based on Field_Negative FILTURB-F52-A-N3-12S2-2018_07 , Removing detections of

## [1] "Eukaryota;Chordata;Amphibia;Anura;NA;NA;NA"

## from

##  [1] "FILTURB-F47-A-N3-12S2-2018_07" "FILTURB-F48-A-N3-12S2-2018_07"
##  [3] "FILTURB-F49-A-N3-12S2-2018_07" "FILTURB-F50-A-N3-12S2-2018_07"
##  [5] "FILTURB-F51-A-N3-12S2-2018_07" "FILTURB-F52-A-N3-12S2-2018_07"
##  [7] "FILTURB-C25-A-N3-12S2-2018_07" "FILTURB-F47-A-N4-12S2-2018_07"
##  [9] "FILTURB-F49-A-N4-12S2-2018_07" "FILTURB-F50-A-N4-12S2-2018_07"
## [11] "FILTURB-F51-A-N4-12S2-2018_07" "FILTURB-F52-A-N4-12S2-2018_07"
## [13] "FILTURB-C25-A-N4-12S2-2018_07" "FILTURB-F48-A-N4-12S2-2018_07"

## which all belong to Site : G09

## 5347 reads removed from 1 detection(s) in 1 sample(s), of which 5347 were in the negative. See table below for details:

## Not printing contamination table

## Based on Field_Negative FILTURB-F64-A-N3-12S2-2018_07 , Removing detections of

## [1] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;Hyla meridionalis"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;NA"

## from

##  [1] "FILTURB-F59-A-N3-12S2-2018_07" "FILTURB-F60-A-N3-12S2-2018_07"
##  [3] "FILTURB-F61-A-N3-12S2-2018_07" "FILTURB-F62-A-N3-12S2-2018_07"
##  [5] "FILTURB-F64-A-N3-12S2-2018_07" "FILTURB-F63-A-N3-12S2-2018_07"
##  [7] "FILTURB-C27-A-N3-12S2-2018_07" "FILTURB-F59-A-N4-12S2-2018_07"
##  [9] "FILTURB-F60-A-N4-12S2-2018_07" "FILTURB-F61-A-N4-12S2-2018_07"
## [11] "FILTURB-F62-A-N4-12S2-2018_07" "FILTURB-F64-A-N4-12S2-2018_07"
## [13] "FILTURB-F63-A-N4-12S2-2018_07" "FILTURB-C27-A-N4-12S2-2018_07"

## which all belong to Site : G60

## 28665 reads removed from 11 detection(s) in 6 sample(s), of which 9554 were in the negative. See table below for details:

## Not printing contamination table

## Based on Field_Negative FILTURB-F64-A-N4-12S2-2018_07 , Removing detections of

## [1] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;Hyla meridionalis"
## [2] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;Hyla;NA"               
## [3] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;NA;NA"

## from

##  [1] "FILTURB-F59-A-N3-12S2-2018_07" "FILTURB-F60-A-N3-12S2-2018_07"
##  [3] "FILTURB-F61-A-N3-12S2-2018_07" "FILTURB-F62-A-N3-12S2-2018_07"
##  [5] "FILTURB-F64-A-N3-12S2-2018_07" "FILTURB-F63-A-N3-12S2-2018_07"
##  [7] "FILTURB-C27-A-N3-12S2-2018_07" "FILTURB-F59-A-N4-12S2-2018_07"
##  [9] "FILTURB-F60-A-N4-12S2-2018_07" "FILTURB-F61-A-N4-12S2-2018_07"
## [11] "FILTURB-F62-A-N4-12S2-2018_07" "FILTURB-F64-A-N4-12S2-2018_07"
## [13] "FILTURB-F63-A-N4-12S2-2018_07" "FILTURB-C27-A-N4-12S2-2018_07"

## which all belong to Site : G60

## 1528 reads removed from 3 detection(s) in 3 sample(s), of which 6786 were in the negative. See table below for details:

## Not printing contamination table

## Based on Field_Negative FILTURB-F76-A-N4-12S2-2018_07 , Removing detections of

## [1] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Lissotriton;Lissotriton helveticus"
## [2] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;Lissotriton;NA"                    
## [3] "Eukaryota;Chordata;Amphibia;Caudata;Salamandridae;NA;NA"

## from

##  [1] "FILTURB-F71-A-N3-12S2-2018_07" "FILTURB-F73-A-N3-12S2-2018_07"
##  [3] "FILTURB-F74-A-N3-12S2-2018_07" "FILTURB-F75-A-N3-12S2-2018_07"
##  [5] "FILTURB-F76-A-N3-12S2-2018_07" "FILTURB-C29-A-N3-12S2-2018_07"
##  [7] "FILTURB-F72-A-N3-12S2-2018_07" "FILTURB-F71-A-N4-12S2-2018_07"
##  [9] "FILTURB-F73-A-N4-12S2-2018_07" "FILTURB-F74-A-N4-12S2-2018_07"
## [11] "FILTURB-F75-A-N4-12S2-2018_07" "FILTURB-F76-A-N4-12S2-2018_07"
## [13] "FILTURB-C29-A-N4-12S2-2018_07" "FILTURB-F72-A-N4-12S2-2018_07"

## which all belong to Site : VB01

## 6918 reads removed from 4 detection(s) in 2 sample(s), of which 6650 were in the negative. See table below for details:

## Not printing contamination table

## Based on Field_Negative FILTURB-F94-A-N3-12S2-2018_07 , Removing detections of

## [1] "Eukaryota;Chordata;Amphibia;Anura;Hylidae;NA;NA"
## [2] "Eukaryota;Chordata;Amphibia;Anura;NA;NA;NA"

## from

##  [1] "FILTURB-F89-A-N3-12S2-2018_07" "FILTURB-F90-A-N3-12S2-2018_07"
##  [3] "FILTURB-F93-A-N3-12S2-2018_07" "FILTURB-F94-A-N3-12S2-2018_07"
##  [5] "FILTURB-C32-A-N3-12S2-2018_07" "FILTURB-F91-A-N3-12S2-2018_07"
##  [7] "FILTURB-F89-A-N4-12S2-2018_07" "FILTURB-F90-A-N4-12S2-2018_07"
##  [9] "FILTURB-F93-A-N4-12S2-2018_07" "FILTURB-F94-A-N4-12S2-2018_07"
## [11] "FILTURB-C32-A-N4-12S2-2018_07" "FILTURB-F91-A-N4-12S2-2018_07"
## [13] "FILTURB-F92-A-N3-12S2-2018_07" "FILTURB-F92-A-N4-12S2-2018_07"

## which all belong to Site : 206b

## 9947 reads removed from 2 detection(s) in 1 sample(s), of which 9947 were in the negative. See table below for details:

## Not printing contamination table

## Based on Extraction_Negative FILTURB-EXTN_B10-A-N3-12S2-2018_07 , Removing detections of

## [1] "Eukaryota;Chordata;Amphibia;Anura;Pelobatidae;Pelobates;Pelobates cultripes"

## from

## character(0)

## which all belong to Site : NA

## 0 reads removed from 0 detection(s) in 0 sample(s), of which 1433 were in the negative. See table below for details:

## Not printing contamination table

## ***********A total of 253151 reads removed